@deksden-com/dd-flow-cli 0.9.0-beta.49 → 0.9.0-beta.52

package/dist/services/runtime-scope-control.js

@@ -4,7 +4,7 @@ import path from "node:path";
 import { createContext } from "../runtime/context.js";
 import { getResourceDatabase } from "../storage/database.js";
 import { AppError } from "../shared/errors.js";
-import { finishManagedProcess, managedProcessBinding, managedProcessStatus, processTreeIsAlive, resourceHome, stopManagedProcess } from "./managed-processes.js";
+import { finishManagedProcess, managedLeaseReleased, managedProcessBinding, managedProcessStatus, processTreeIsAlive, resourceHome, stopManagedProcess } from "./managed-processes.js";
 import { requestRuntimeScopeControl, runtimeBudgetStatus, scopeLocalProcessRole, validateRuntimeScopeManifest } from "./runtime-budget.js";
 import { nativeInventoryVersion, recordRunControlIntent, retainedDaemonOperations, runControlStatus } from "./run-control.js";
 import { requestRunControl } from "./run-control-worker.js";
@@ -125,7 +125,7 @@ export function retainScopeDrain(context, control, processes, runs, native, prob
 }
 export function scopeRunProcessEvidence(record, runs, registryHome) {
     const metadata = JSON.parse(record.metadata_json);
-    if (!record.pid || !record.pid_started_at || !record.project_id || !record.run_id || !metadata.dd_flow_home)
+    if ((!managedLeaseReleased(record) && (!record.pid || !record.pid_started_at)) || !record.project_id || !record.run_id || !metadata.dd_flow_home)
         return null;
     for (const run of runs) {
         if (run.runtime_home !== metadata.dd_flow_home || run.project_id !== record.project_id || run.run_id !== record.run_id)

package/dist/services/runtime-scope-stop.js

@@ -3,7 +3,7 @@ import fs from "node:fs";
 import path from "node:path";
 import { AppError } from "../shared/errors.js";
 import { runHarnessAdapter } from "./harness-adapter.js";
-import { managedProcessBinding, managedProcessStatus, processIsAlive, processTreeIsAlive, resourceHome, stopManagedProcess } from "./managed-processes.js";
+import { managedLeaseReleased, managedProcessBinding, managedProcessStatus, processIsAlive, processTreeIsAlive, resourceHome, stopManagedProcess } from "./managed-processes.js";
 import { fenceRuntimeBudget, runtimeBudgetStatus, scopeLocalProcessRole } from "./runtime-budget.js";
 import { retainedDaemonOperations } from "./run-control.js";
 import { historicalDaemonSettlement } from "./native-daemon-history.js";
@@ -62,6 +62,10 @@ export async function stopRuntimeScope(context, scopeId, requestId) {
     for (const record of runtimeBudgetStatus(context, scopeId).processes) {
         if (covered.has(record.id))
             continue;
+        if (managedLeaseReleased(record)) {
+            nodes.push({ process_id: record.id, settled: true });
+            continue;
+        }
         const metadata = JSON.parse(record.metadata_json);
         // RUN control owns active controllers/checks. Adopt only its already-finished
         // physical registrations here; death alone is not a completed RUN operation.

package/dist/services/usage.js

@@ -165,7 +165,7 @@ export function recalculateRunUsage(context, input) {
     const usageFinal = final && unsettledSessions.length === 0;
     const persistRunProjection = !input.sessionId && !input.stage;
     if (persistRunProjection) {
-        context.db.exec("BEGIN IMMEDIATE");
+        context.db.exec("SAVEPOINT run_usage");
         try {
             context.db.run("DELETE FROM usage WHERE project_id = ? AND run_id = ?", [input.projectId, input.runId]);
             for (const row of rows) {
@@ -185,10 +185,11 @@ export function recalculateRunUsage(context, input) {
             AND status = 'idle'
             AND NOT EXISTS (SELECT 1 FROM work_sessions WHERE session_id = ? AND status = 'running')`, [observedAt, session.completed_at, input.projectId, input.runId, session.session_id, session.session_id]);
             }
-            context.db.exec("COMMIT");
+            context.db.exec("RELEASE run_usage");
         }
         catch (error) {
-            context.db.exec("ROLLBACK");
+            context.db.exec("ROLLBACK TO run_usage");
+            context.db.exec("RELEASE run_usage");
             throw error;
         }
     }

package/dist/services/vnext-code-review.js

@@ -10,15 +10,17 @@ import { validateSchema } from "./schema-validation.js";
 import { flowCommand } from "./stage-pause.js";
 import { assertStageStartHookEvent } from "./hooks.js";
 import { requireVnextWorkspaceRoute } from "./vnext-workspace-policy.js";
-import { addVnextCodeRepair } from "./vnext-code.js";
-import { finalCodeCheckDeclarations, runCodeChecks, unchangedFinalGateFailures, validateFailedCheckRetry, workspaceFingerprint } from "./code-checks.js";
-import { addWorkBatch, bindStageCoordinatorWork, finishWork, refreshRunWorkProjection } from "./work-registry.js";
+import { addVnextCodeRepair, resumeAcceptedCodeStage } from "./vnext-code.js";
+import { finalCodeCheckDeclarations, runCodeChecks, validateFailedCheckRetry, workspaceFingerprint } from "./code-checks.js";
+import { addWorkBatch, bindStageCoordinatorWork, finishStageCoordinatorWork, refreshRunWorkProjection } from "./work-registry.js";
+import { withStageSettlement } from "./runs.js";
 import { vnextStageDirectory } from "../domain/stage-catalog.js";
 import { writeStageReport } from "./stage-report-renderer.js";
 import { applyExternalStageContext } from "./stage-context.js";
 import { readFanoutDescriptor, writeFanoutDescriptor } from "./vnext-fanout.js";
 import { ensureVnextMergeRequest } from "./vnext-merge.js";
 import { validateVnextCodeHandoff } from "./vnext-plan.js";
+import { assertRunMutationAllowed } from "./run-recovery.js";
 const stage = "code-review";
 const stageDir = vnextStageDirectory(stage);
 const baselineAspects = ["goal_traceability", "coding_standards_design_review", "verification_evidence_review"];
@@ -123,6 +125,7 @@ export async function finishVnextCodeReview(context, input) {
     const mode = reviewContext.mode;
     if (!mode)
         throw new AppError("runtime_missing", "CODE-REVIEW effective mode was not frozen at stage start", 1);
+    const generation = assertRunMutationAllowed(context, project.id, run.id);
     if (reviewContext.code_report_sha256 !== sha256File(path.join(home, "05-code", "stage-report.json")))
         throw new AppError("code_review_input_changed", "Accepted CODE report changed after CODE-REVIEW start", 2);
     const handoffFailures = validateVnextCodeHandoff(context, { projectRoot, workspaceRoot: run.workspace_root, runId: run.id, home });
@@ -131,7 +134,9 @@ export async function finishVnextCodeReview(context, input) {
     const reportPath = path.join(root, "stage-report.json");
     if (stageStatus(run, stage) === "done" && fs.existsSync(reportPath)) {
         const report = readJson(reportPath);
-        return { ok: true, resumed: true, run_id: run.id, stage, outcome: "accepted", report_path: reportPath, next_action: report.semantic?.next_action ?? "code_review_completed" };
+        const next = report.semantic?.next_action ?? "code_review_completed";
+        resumeAcceptedCodeStage(context, run, projectRoot, stage, report, next);
+        return { ok: true, resumed: true, run_id: run.id, stage, outcome: "accepted", report_path: reportPath, next_action: next };
     }
     const rootWork = requireRootWork(context, project.id, run.id);
     const coordinator = context.db.get("SELECT session_id, result_path FROM work_sessions WHERE work_id = ? AND status = 'running' ORDER BY created_at DESC LIMIT 1", [rootWork.work_id]);
@@ -145,6 +150,7 @@ export async function finishVnextCodeReview(context, input) {
     const cycle = reviewContext.cycle ?? "initial";
     const reviewers = reviewerWorks(context, project.id, run.id, cycle);
     if (mode !== "off") {
+        assertCodeReviewCoverage(reviewGroups(home), reviewers);
         const incomplete = reviewers.filter((work) => work.status !== "completed");
         if (incomplete.length)
             throw new AppError("reviewer_jobs_incomplete", "CODE-REVIEW cannot finish while reviewer Work is unsettled", 2, { works: incomplete.map((work) => ({ work_id: work.work_id, status: work.status })) });
@@ -173,13 +179,10 @@ export async function finishVnextCodeReview(context, input) {
     const repairs = reviewRepairWorks(context, project.id, run.id, root, cycle);
     const finalChecks = finalCodeCheckDeclarations(run.workspace_root, codeWorks(context, project.id, run.id).flatMap((work) => { const payload = readJsonString(work.payload_json); return Array.isArray(payload.checks) ? payload.checks : []; }));
     if (input.retryCheckId) {
-        validateFailedCheckRetry(context, { projectId: project.id, runId: run.id, receiptId: input.retryCheckId, declarations: finalChecks, artifactRoot: path.join(requireHome(run), stageDir), reason: input.retryReason });
+        validateFailedCheckRetry(context, { projectId: project.id, runId: run.id, receiptId: input.retryCheckId, declarations: finalChecks, reason: input.retryReason });
         appendFlowRunTimelineEvent(context, project.id, run.id, { type: "check_retry_requested", check_receipt_id: input.retryCheckId, stage, reason: input.retryReason ?? "operator retry" });
     }
-    const unchangedFailures = unchangedFinalGateFailures(context, { projectId: project.id, runId: run.id, workspaceRoot: run.workspace_root, declarations: finalChecks, ...(input.retryCheckId ? { retryReceiptId: input.retryCheckId } : {}) });
-    if (unchangedFailures.length)
-        throw new AppError("code_review_gate_repair_required", "CODE-REVIEW final gate already failed for the unchanged workspace; choose source repair or restore the environment and retry that receipt", 2, { outcome: "repair_required", retry_after_workspace_change: true, workspace_fingerprint: unchangedFailures[0].workspace_fingerprint, failures: unchangedFailures, retry_command: `${finishCommand(context, run.id, projectRoot, decisionFile)} --retry-check ${unchangedFailures[0].id} --reason "<environment recovery evidence>"` });
-    const receipts = await runCodeChecks(context, { projectId: project.id, runId: run.id, runHome: home, workspaceRoot: run.workspace_root, artifactDir: stageDir, scope: "aggregate", checks: finalChecks, ...(input.progress ? { progress: input.progress } : {}) });
+    const receipts = await runCodeChecks(context, { projectId: project.id, runId: run.id, runHome: home, workspaceRoot: run.workspace_root, artifactDir: stageDir, scope: "aggregate", checks: finalChecks, ...(input.retryCheckId ? { retryReceiptId: input.retryCheckId, retryReason: input.retryReason } : {}), ...(input.progress ? { progress: input.progress } : {}) });
     const failed = receipts.filter((receipt) => receipt.status !== "passed");
     if (failed.length)
         throw new AppError("code_review_gate_failed", "CODE-REVIEW repair changed the project but the aggregate gate failed", 2, {
@@ -200,18 +203,21 @@ export async function finishVnextCodeReview(context, input) {
     const acceptedPaths = changedPaths(run.workspace_root);
     const mergeRequest = nextAction === "start_merge" ? ensureVnextMergeRequest(context, { projectRoot, runId: run.id, acceptedPaths }) : null;
     writeReport(root, report);
-    completeFlowRunStage(context, { projectRoot, runId: run.id, stage, status: "done", data: "stage-report.json", dataSchemaId: "dd-flow/stage-report@1", report: "stage-report.md", stageReport: "stage-report.html" });
-    appendFlowRunTimelineEvent(context, project.id, run.id, { type: "code_review_completed", work_id: rootWork.work_id, outcome });
-    if (nextAction === "start_merge")
-        advanceFlowRun(context, { settlementStage: "code-review", projectRoot, runId: run.id, status: "running", verdict: "code_review_completed", nextAction });
-    else {
-        await finishWork(context, rootWork.work_id, JSON.stringify(report, null, 2));
-        completeFlowRun(context, { projectRoot, runId: run.id, status: "done", verdict: "code_review_completed", nextAction: undefined });
-    }
-    refreshRunWorkProjection(context, project.id, run.id);
+    withStageSettlement(context, () => {
+        assertRunMutationAllowed(context, project.id, run.id, generation);
+        completeFlowRunStage(context, { projectRoot, runId: run.id, stage, status: "done", data: "stage-report.json", dataSchemaId: "dd-flow/stage-report@1", report: "stage-report.md", stageReport: "stage-report.html" });
+        appendFlowRunTimelineEvent(context, project.id, run.id, { type: "code_review_completed", work_id: rootWork.work_id, outcome });
+        if (nextAction === "start_merge")
+            advanceFlowRun(context, { settlementStage: "code-review", projectRoot, runId: run.id, status: "running", verdict: "code_review_completed", nextAction });
+        else {
+            finishStageCoordinatorWork(context, rootWork.work_id, JSON.stringify(report, null, 2));
+            completeFlowRun(context, { projectRoot, runId: run.id, status: "done", verdict: "code_review_completed", nextAction: undefined });
+        }
+        refreshRunWorkProjection(context, project.id, run.id);
+    });
     return { ok: true, run_id: run.id, stage, outcome, report_path: path.join(root, "stage-report.json"), next_action: nextAction, ...(mergeRequest ? { merge_request: mergeRequest, next: { kind: "start_stage", stage: "merge", command: `${flowCommand(context)} stage start ${run.id} --stage merge --project-root ${JSON.stringify(projectRoot)} --json --progress-jsonl` } } : {}) };
 }
-function reviewGroups(home) {
+export function reviewGroups(home) {
     const expected = new Set(baselineAspects);
     const declared = [];
     for (const file of findFiles(path.join(home, "03-plan"), "aspect-map.json")) {
@@ -226,15 +232,33 @@ function reviewGroups(home) {
     if (!declared.length)
         return [{ key: "baseline", aspect_ids: [...expected].sort() }];
     const assigned = new Set();
+    const scoped = new Set();
     for (const group of declared)
         for (const aspectId of group.aspect_ids) {
-            if (assigned.has(aspectId))
-                throw new AppError("code_review_groups_invalid", "A CODE-REVIEW aspect appears in more than one accepted group", 2, { aspect_id: aspectId });
+            const assignment = `${group.key.slice(0, group.key.lastIndexOf("/"))}/${aspectId}`;
+            if (scoped.has(assignment))
+                throw new AppError("code_review_groups_invalid", "A CODE-REVIEW aspect appears in more than one group of the same protocol", 2, { aspect_id: aspectId });
+            scoped.add(assignment);
             assigned.add(aspectId);
         }
     const missing = [...expected].filter((aspectId) => !assigned.has(aspectId)).sort();
     return [...declared, ...(missing.length ? [{ key: "baseline", aspect_ids: missing }] : [])];
 }
+export function assertCodeReviewCoverage(groups, reviewers) {
+    const expected = new Map(groups.map(group => [group.key, [...group.aspect_ids].sort()]));
+    if (!expected.size || expected.size !== groups.length)
+        throw new AppError("reviewer_coverage_invalid", "CODE-REVIEW expected group identities must be nonempty and unique", 2);
+    const seen = new Set();
+    for (const work of reviewers) {
+        const group = readJsonString(work.payload_json).group;
+        if (!group?.key || seen.has(group.key) || !expected.has(group.key) || !Array.isArray(group.aspect_ids) || JSON.stringify([...group.aspect_ids].sort()) !== JSON.stringify(expected.get(group.key)))
+            throw new AppError("reviewer_coverage_invalid", "CODE-REVIEW Work does not match its expected group", 2, { work_id: work.work_id });
+        seen.add(group.key);
+    }
+    const missing = [...expected.keys()].filter(key => !seen.has(key));
+    if (missing.length || !expected.size)
+        throw new AppError("reviewer_coverage_invalid", "CODE-REVIEW requires every expected reviewer group", 2, { missing_groups: missing });
+}
 export function reviewerTask(home, group) { return `Read-only independent CODE review for ${group.key}. Assess every assigned aspect exactly once: ${group.aspect_ids.join(", ")}. Read the accepted PLAN, ${path.join(home, "05-code", "stage-report.json")}, and any files needed under the bounded CODE evidence root ${path.join(home, "05-code")}. Verify that universal and exclusive constraints (only, any, all, never, whole) and stated exceptions were not narrowed. For every changed mutation guarded by membership, ownership, authorization or parent lifecycle state, trace the decision to the write boundary: the predicate must remain in the write statement or the guard and write must share one explicit transaction with the needed lock. A separate earlier read is not proof of current authority or lifecycle state; report a material finding when this invariant is broken. Evidence closes a claim only when it exercises the named failure mechanism; a sequential negative test does not prove a concurrency race, and proof limits cannot waive an accepted obligation. Report only material, evidenced defects: a violated obligation or rule, direct evidence, impact, and minimum required outcome. Do not report taste, cosmetics, or untargeted refactoring. Use local finding ids FIND-001, FIND-002, and so on; dd-flow adds the Work-qualified canonical reference. Return dd-flow/code-review-result@1.`; }
 function orchestratorPrompt(context, input) { const template = read(path.join(input.run.workspace_root, ".memory-bank", "dd-flow", "vnext", "code-review.md")); const decision = path.join(input.root, "decision.json"); const checks = acceptedCodeChecks(context, input.run.project_id, input.run.id).map(({ id, purpose }) => ({ id, purpose })); return ["<stage_identity>", `- RUN: ${input.run.id}`, `- root Work: ${input.rootWork.work_id}`, `- stage: ${stage}`, `- mode: ${input.mode}`, "</stage_identity>", "", "<trusted_runtime_context>", `- project root: ${input.projectRoot}`, `- immutable write workspace: ${input.run.workspace_root}`, `- stage workspace: ${input.root}`, `- bounded CODE evidence root: ${path.join(input.run.run_root, "05-code")}`, "CODE is already semantically verified and all declared checks passed. Do not redo CODE verification; conduct independent quality review.", "</trusted_runtime_context>", "", "<review_groups>", ...input.groups.map((group) => `- ${group.key}: ${group.aspect_ids.join(", ")}`), "</review_groups>", "", "<execution_commands>", "Each reviewer Work must run in one fresh child session. The coordinator must never claim a reviewer Work itself. Start each ready Work with its exact start_command from the work graph; it receives the task and result schema. Reviewers are read-only and must not create subagents. Do not interrupt a quiet worker.", `Ready reviewer Works: ${flowCommand(context)} work ls --run ${input.run.id} --ready --project-root ${JSON.stringify(input.projectRoot)} --json`, `Finish only after every reviewer Work settles and you have written ${decision}: ${finishCommand(context, input.run.id, input.projectRoot, decision)}`, "Reviewer results use local FIND-NNN ids. Classify them by the canonical WRK-.../FIND-NNN finding_ref returned by dd-flow. Fix P0/P1. Fix bounded safe P2 by default; defer only a legitimate P2 with a named DEF. P3 is an observation or a reasoned rejection, not automatic repair/DEF. For every disposition fix, check_refs is mandatory: choose the one or more causal checks from the accepted list below that the repair must rerun. Do not guess a CHK id or copy every check. The first successful Finish freezes this decision and creates one repair Work when needed. Run it, then call the same Finish command again. Review is not repeated.", "If the post-repair aggregate gate fails, do not stop after `code_review_gate_failed`: that rejected finish does not create a repair Work. In the same coordinator Turn, use the returned repair command with the failed receipt, a relevant completed origin Work ID, and a concise repair objective; then stop so the runner can dispatch the new repair. Do not edit invisibly in the root orchestrator.", `Accepted repair checks: ${JSON.stringify(checks)}`, "```json", JSON.stringify({ schema_id: "dd-flow/code-review-decision@3", summary: "Evidence-backed conclusion.", findings: [{ finding_ref: "WRK-001-review/FIND-001", disposition: "fix | defer | reject | duplicate", reason: "Why this classification is correct.", check_refs: ["CHK-CAUSAL-CHECK only when disposition is fix"], def_id: "DEF-0001 only for an allowed P2 deferral", duplicate_of: "canonical finding_ref only for duplicate" }] }, null, 2), "```", "</execution_commands>", "", "<stage_instructions>", template, "</stage_instructions>", ""].join("\n"); }
 function canonicalReviewEvidence(decision, reviewers) {

package/dist/services/vnext-code.js

@@ -4,21 +4,22 @@ import fs from "node:fs";
 import path from "node:path";
 import { AppError } from "../shared/errors.js";
 import { resolveProjectRoot } from "../storage/paths.js";
-import { aggregateCheckDeclarations, checkReceipts, effectiveCheckDeclarations, finalCodeCheckDeclarations, runCodeChecks, unchangedFinalGateFailures, validateFailedCheckRetry, workspaceChangedPaths, workspaceFingerprint } from "./code-checks.js";
+import { aggregateCheckDeclarations, effectiveCheckDeclarations, finalCodeCheckDeclarations, runCodeChecks, validateFailedCheckRetry, workspaceChangedPaths } from "./code-checks.js";
 import { requireProjectByRoot } from "./projects.js";
-import { appendFlowRunTimelineEvent, advanceFlowRun, attachFlowRunStage, completeFlowRunStage, completeFlowRun, getFlowRunVariables, gitFacts } from "./runs.js";
+import { appendFlowRunTimelineEvent, advanceFlowRun, attachFlowRunStage, completeFlowRunStage, completeFlowRun, withStageSettlement, getFlowRunVariables, gitFacts } from "./runs.js";
 import { validateSchema } from "./schema-validation.js";
 import { flowCommand } from "./stage-pause.js";
 import { validateVnextCodeHandoff } from "./vnext-plan.js";
 import { requireVnextWorkspaceRoute } from "./vnext-workspace-policy.js";
 import { readVnextSpecifyResult } from "./vnext-specify.js";
-import { addWorkBatch, bindStageCoordinatorWork, codeWorkGraph, finishWork, refreshRunWorkProjection, validateWorkBatchFile, workStartCommand } from "./work-registry.js";
+import { addWorkBatch, bindStageCoordinatorWork, codeWorkGraph, finishStageCoordinatorWork, refreshRunWorkProjection, validateWorkBatchFile, workStartCommand } from "./work-registry.js";
 import { vnextStageDirectory } from "../domain/stage-catalog.js";
 import { writeStageReport } from "./stage-report-renderer.js";
 import { ensureVnextMergeRequest } from "./vnext-merge.js";
 import { assertStageStartHookEvent } from "./hooks.js";
 import { applyExternalStageContext } from "./stage-context.js";
 import { readFanoutDescriptor, writeFanoutDescriptor } from "./vnext-fanout.js";
+import { assertRunMutationAllowed } from "./run-recovery.js";
 const stage = "code";
 const stageDir = vnextStageDirectory("code");
 export async function startVnextCode(context, input) {
@@ -36,6 +37,7 @@ export async function startVnextCode(context, input) {
         const externalContext = applyExternalStageContext({ stageRoot: existingRoot, promptPath: existingPrompt, ...(input.externalContext ? { loaded: input.externalContext } : {}) });
         const prompt = fs.readFileSync(existingPrompt, "utf8");
         const rootWork = requireRootWork(context, project.id, input.runId);
+        bindStageCoordinatorWork(context, { workId: rootWork.work_id, hookEventId: input.hookEventId, stage, promptPath: existingPrompt, resultPath: path.join(existingRoot, "stage-report.json"), ...(input.contextSha256 ? { contextSha256: input.contextSha256 } : {}) });
         const orchestration = readFanoutDescriptor(existingRoot) ?? writeFanoutDescriptor(existingRoot, { stage, parent_work_id: rootWork.work_id, dispatch: "none", capacity_required: true });
         return { ok: true, resumed: true, run_id: run.id, stage, stage_status: existingStage, prompt_path: existingPrompt, worker_prompt_markdown: prompt, ...(externalContext ? { external_context: externalContext } : {}), orchestration, graph: codeWorkGraph(context, project.id, run.id), next: { refresh_graph_command: `${flowCommand(context)} work ls --run ${run.id} --ready --project-root ${JSON.stringify(projectRoot)} --json`, finish_command: finishCommand(context, input.runId, projectRoot, path.join(existingRoot, "code-verification.json")) } };
     }
@@ -108,8 +110,10 @@ export async function finishVnextCode(context, input) {
     const run = requireRun(context, project.id, input.runId);
     const home = requireHome(run);
     const root = path.join(home, stageDir);
+    const generation = assertRunMutationAllowed(context, project.id, run.id);
     requireVnextWorkspaceRoute({ projectRoot, runId: run.id, runHome: home, workspaceRoot: run.workspace_root, stage });
     if (stageStatus(run, stage) === "done" && fs.existsSync(path.join(root, "stage-report.json"))) {
+        resumeAcceptedCodeStage(context, run, projectRoot, stage, JSON.parse(fs.readFileSync(path.join(root, "stage-report.json"), "utf8")), nextAction(run, changedPathsFromReport(path.join(root, "stage-report.json"))));
         return { ok: true, resumed: true, run_id: run.id, stage, outcome: "accepted", report_path: path.join(root, "stage-report.json"), next_action: nextAction(run, changedPathsFromReport(path.join(root, "stage-report.json"))) };
     }
     const handoffFailures = validateVnextCodeHandoff(context, {
@@ -158,32 +162,14 @@ export async function finishVnextCode(context, input) {
     }
     const checks = finalCodeCheckDeclarations(run.workspace_root, works.flatMap((work) => packet(work)?.checks ?? []));
     if (input.retryCheckId) {
-        validateFailedCheckRetry(context, { projectId: project.id, runId: run.id, receiptId: input.retryCheckId, declarations: checks, artifactRoot: path.join(requireHome(run), stageDir), reason: input.retryReason });
+        validateFailedCheckRetry(context, { projectId: project.id, runId: run.id, receiptId: input.retryCheckId, declarations: checks, reason: input.retryReason });
         appendFlowRunTimelineEvent(context, project.id, run.id, { type: "check_retry_requested", check_receipt_id: input.retryCheckId, stage, reason: input.retryReason ?? "operator retry" });
     }
-    const unchangedFailures = unchangedFinalGateFailures(context, { projectId: project.id, runId: run.id, workspaceRoot: run.workspace_root, declarations: checks, ...(input.retryCheckId ? { retryReceiptId: input.retryCheckId } : {}) });
-    if (unchangedFailures.length)
-        throw new AppError("code_gate_repair_required", "CODE final gate already failed for the unchanged workspace; choose source repair or restore the environment and retry that receipt", 2, { outcome: "repair_required", retry_after_workspace_change: true, workspace_fingerprint: unchangedFailures[0].workspace_fingerprint, failures: unchangedFailures, retry_command: `${finishCommand(context, run.id, projectRoot, input.verificationFile)} --retry-check ${unchangedFailures[0].id} --reason "<environment recovery evidence>"` });
-    let receipts = reusableAggregateGateReceipts(context, { projectId: project.id, runId: run.id, workspaceRoot: run.workspace_root, checks });
-    if (!receipts) {
-        const release = acquireAggregateGateLock(root);
-        try {
-            // A prior caller may have completed the slow gate while this caller was
-            // waiting to acquire the lock. Reuse that immutable evidence.
-            receipts = reusableAggregateGateReceipts(context, { projectId: project.id, runId: run.id, workspaceRoot: run.workspace_root, checks }) ?? await runCodeChecks(context, {
-                projectId: project.id,
-                runId: run.id,
-                runHome: home,
-                workspaceRoot: run.workspace_root,
-                scope: "aggregate",
-                checks,
-                ...(input.progress ? { progress: input.progress } : {})
-            });
-        }
-        finally {
-            release();
-        }
-    }
+    const receipts = await runCodeChecks(context, {
+        projectId: project.id, runId: run.id, runHome: home, workspaceRoot: run.workspace_root, scope: "aggregate", checks,
+        ...(input.retryCheckId ? { retryReceiptId: input.retryCheckId, retryReason: input.retryReason } : {}),
+        ...(input.progress ? { progress: input.progress } : {})
+    });
     const failed = receipts.filter((receipt) => receipt.status !== "passed");
     if (failed.length) {
         throw new AppError("code_gate_failed", "CODE remains running because the aggregate project gate failed", 2, {
@@ -195,9 +181,8 @@ export async function finishVnextCode(context, input) {
             retry_command: `${finishCommand(context, run.id, projectRoot, input.verificationFile)} --retry-check ${failed[0].id} --reason "<environment recovery evidence>"`
         });
     }
-    const allReceipts = checkReceipts(context, { projectId: project.id, runId: run.id });
-    const finalReceipts = latestReceiptsByCommand(allReceipts);
-    const projectedVerification = verificationProjection(works, finalReceipts, { historicalReceipts: allReceipts, runId: run.id, runHome: home });
+    const finalReceipts = receipts;
+    const projectedVerification = verificationProjection(works, finalReceipts, { historicalReceipts: finalReceipts, runId: run.id, runHome: home });
     const unresolvedAcceptance = (projectedVerification.acceptance ?? []).filter((item) => item.status === "unresolved");
     if (unresolvedAcceptance.length)
         throw new AppError("code_acceptance_unresolved", "CODE cannot finish until every due acceptance criterion has current checks and evidence", 2, { unresolved: unresolvedAcceptance });
@@ -249,29 +234,32 @@ export async function finishVnextCode(context, input) {
     // so an invalid merge policy leaves CODE safely running and retryable.
     const mergeRequest = next === "start_merge" ? ensureVnextMergeRequest(context, { projectRoot, runId: run.id, acceptedPaths: changedPaths }) : null;
     writeReport(root, report);
-    completeFlowRunStage(context, {
-        projectRoot,
-        runId: run.id,
-        stage,
-        status: "done",
-        data: "stage-report.json",
-        dataSchemaId: "dd-flow/stage-report@1",
-        report: "stage-report.md",
-        stageReport: "stage-report.html"
-    });
-    const rootWork = requireRootWork(context, project.id, run.id);
-    appendFlowRunTimelineEvent(context, project.id, run.id, {
-        type: "code_accepted",
-        work_id: rootWork.work_id,
-        checks: finalReceipts.map((receipt) => receipt.id)
+    withStageSettlement(context, () => {
+        assertRunMutationAllowed(context, project.id, run.id, generation);
+        completeFlowRunStage(context, {
+            projectRoot,
+            runId: run.id,
+            stage,
+            status: "done",
+            data: "stage-report.json",
+            dataSchemaId: "dd-flow/stage-report@1",
+            report: "stage-report.md",
+            stageReport: "stage-report.html"
+        });
+        const rootWork = requireRootWork(context, project.id, run.id);
+        appendFlowRunTimelineEvent(context, project.id, run.id, {
+            type: "code_accepted",
+            work_id: rootWork.work_id,
+            checks: finalReceipts.map((receipt) => receipt.id)
+        });
+        if (next === "code_completed") {
+            finishStageCoordinatorWork(context, rootWork.work_id, JSON.stringify(report, null, 2));
+            completeFlowRun(context, { projectRoot, runId: run.id, status: "done", verdict: "code_completed", nextAction: undefined });
+        }
+        else {
+            advanceFlowRun(context, { settlementStage: "code", projectRoot, runId: run.id, status: "running", verdict: "code_completed", nextAction: next });
+        }
     });
-    if (next === "code_completed") {
-        await finishWork(context, rootWork.work_id, JSON.stringify(report, null, 2));
-        completeFlowRun(context, { projectRoot, runId: run.id, status: "done", verdict: "code_completed", nextAction: undefined });
-    }
-    else {
-        advanceFlowRun(context, { settlementStage: "code", projectRoot, runId: run.id, status: "running", verdict: "code_completed", nextAction: next });
-    }
     return {
         ok: true,
         run_id: run.id,
@@ -477,76 +465,6 @@ function coordinatorPrompt(context, input) {
 export function profileCommands(workspaceRoot) {
     return aggregateCheckDeclarations(workspaceRoot).map((check) => check.command);
 }
-function latestReceiptsByCommand(receipts) {
-    const latest = new Map();
-    for (const receipt of receipts)
-        for (const ref of receipt.check_refs)
-            latest.set(ref, receipt);
-    return [...new Set(latest.values())];
-}
-/**
- * A CODE finish may be retried after a client loses the long command's output.
- * Reusing complete, same-workspace receipts is correct; rerunning them is both
- * expensive and can race the still-settling original invocation.
- */
-export function reusableAggregateGateReceipts(context, input) {
-    const expected = new Set(input.checks.map((check) => check.id));
-    const current = workspaceFingerprint(input.workspaceRoot);
-    const latest = new Map();
-    for (const receipt of checkReceipts(context, { projectId: input.projectId, runId: input.runId })) {
-        if (receipt.scope === "aggregate")
-            for (const ref of receipt.check_refs)
-                if (expected.has(ref))
-                    latest.set(ref, receipt);
-    }
-    if (latest.size !== expected.size)
-        return null;
-    const receipts = input.checks.map((check) => latest.get(check.id));
-    return receipts.every((receipt) => receipt.status === "passed" && receipt.workspace_fingerprint === current) ? receipts : null;
-}
-/** One aggregate gate per RUN; a second invocation must wait, never duplicate it. */
-function acquireAggregateGateLock(root) {
-    const directory = path.join(root, "checks");
-    const lock = path.join(directory, ".aggregate-gate.lock");
-    fs.mkdirSync(directory, { recursive: true });
-    try {
-        const descriptor = fs.openSync(lock, "wx");
-        fs.writeFileSync(descriptor, JSON.stringify({ pid: process.pid, started_at: new Date().toISOString() }));
-        fs.closeSync(descriptor);
-    }
-    catch (error) {
-        if (!isExistingLock(error))
-            throw error;
-        const activePid = lockPid(lock);
-        if (activePid && processAlive(activePid)) {
-            throw new AppError("code_gate_in_progress", "CODE aggregate gate is already running; wait for that exact stage finish command to return", 1, { pid: activePid, lock });
-        }
-        fs.rmSync(lock, { force: true });
-        return acquireAggregateGateLock(root);
-    }
-    return () => fs.rmSync(lock, { force: true });
-}
-function isExistingLock(error) {
-    return Boolean(error && typeof error === "object" && error.code === "EEXIST");
-}
-function lockPid(lock) {
-    try {
-        const parsed = JSON.parse(fs.readFileSync(lock, "utf8"));
-        return Number.isInteger(parsed.pid) && Number(parsed.pid) > 0 ? Number(parsed.pid) : null;
-    }
-    catch {
-        return null;
-    }
-}
-function processAlive(pid) {
-    try {
-        process.kill(pid, 0);
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
 /**
  * The immutable Work result is a repair history. The stage report is a current
  * acceptance projection, so a registered receipt from an older check epoch
@@ -770,6 +688,28 @@ function uniqueBy(values, key) {
         return true;
     });
 }
+/** Repair pre-atomic terminal stages without repeating accepted checks or rewinding a successor. */
+export function resumeAcceptedCodeStage(context, run, projectRoot, stage, report, next) {
+    const index = JSON.parse(run.index_json);
+    if ((index.current_stage ?? index.stage_runs.at(-1)?.stage) !== stage)
+        return;
+    const terminal = next === "code_completed" || next === "code_review_completed";
+    if (!terminal && index.next_action === next)
+        return;
+    withStageSettlement(context, () => {
+        if (!terminal) {
+            advanceFlowRun(context, { settlementStage: stage, projectRoot, runId: run.id, status: "running", verdict: `${stage.replaceAll("-", "_")}_completed`, nextAction: next });
+            return;
+        }
+        const work = context.db.get("SELECT * FROM works WHERE project_id = ? AND run_id = ? AND parent_work_id IS NULL ORDER BY created_at LIMIT 1", [run.project_id, run.id]);
+        if (!work)
+            throw new AppError("runtime_missing", "Accepted stage has no root coordinator", 1);
+        if (work.status !== "completed")
+            finishStageCoordinatorWork(context, work.work_id, JSON.stringify(report, null, 2));
+        if (index.status !== "done")
+            completeFlowRun(context, { projectRoot, runId: run.id, status: "done", verdict: next });
+    });
+}
 function writeReport(root, report) {
     writeStageReport(root, report);
 }